Many of the member clubs have performed well when competing against SFL clubs in the Scottish Cup. However, from the 1990s onwards, the HFL has been a victim of its own success, with various teams defecting to other leagues. Furthermore it has also had to contend with overexposure of large teams in the area, such as Aberdeen and Inverness Caledonian Thistle, as well as the Old Firm to the South, and to an extent English football. However, the lack of Premier League, and to a lesser extent First Division, teams in the area, has worked in its favour, with some football fans being less willing to travel long distances to games in southern Scotland.

The league has been somewhat weakened in recent years by the departure of many former members who have subsequently joined the SFL. This happened in 1994 when Caledonian, Inverness Thistle and Ross County left. Until then the HFL had operated with 18 clubs; this was reduced by the departure of the three mentioned clubs, but Wick Academy from the North Caledonian Football League were elected, to create a league of 16 clubs. This was the state of affairs till 2000 when Elgin City and Peterhead were elected into the SFL. In 2002 Inverurie Loco Works were elected into the HFL to give it a membership of 15 clubs, with which it continues to operate.

In 2008, North Region Junior League sides Formartine United and Turriff United both submitted bids to join the Highland League, following in the footsteps of past Junior League side Inverurie Locos. If both teams were to join, the Highland League would have a total of 17 teams. An even team league is preferred, so only one club's application was likely to be successful. Whichever team is successful in their application was planned to join in the 2009–10 season. However Banks O' Dee and Strathspey Thistle also applied, giving the potential for an 18 team Highland league in 2009-10 if three of these four clubs were elected. On February 25 2009, Formartine United, Turriff United and Strathspey Thistle were accepted into the league for the following season, with Banks O' Dee being the unsuccessful club.

Results from the HFL and the Highland League Cup have featured on the Press Association vidiprinter since the start of the 1997–98 season.

The Highland League is the subject of a song of the same name by the popular music ensemble I, Ludicrous.[1]